Students Making History

By Mary Alice Hartsock

If you have been a student, you’ve probably struggled to decipher the handwriting of a teacher or professor. When you’re truly stuck, you can usually follow up with your instructor in person. But what if you couldn’t ask the writer about their bewildering scribbles, and your ability to decipher their notes could shape a part of scientific history?

Drexel University students Nicholas Blase and Valerie Coghlan faced this problem while working in the Academy’s Botany Collection. Their job was to examine images of printed or handwritten labels and packets holding lichens and bryophytes and enter information from these labels into a searchable database. Part of a larger process known as digitization, this work puts Academy specimen data at the fingertips of scientists around the world.

Each day, Blase and Coghlan worked to database 200 specimens using software that “reads” typed images of specimen labels.

“This goal was often met as long as there were no troublesome labels,” says Blase. “But common slowdowns included getting caught up on deciphering handwriting for a large string of specimens.”

Chocolate Chip Lichen
Chocolate Chip Lichen: Solorina saccata (L.) Ach. This lichen grows in crevices and moist, sheltered areas, especially on calcium carbonate-rich rocks and soils. Its range stretches from the mountains of the Mediterranean to the Arctic.

In most cases, Blase and Coghlan couldn’t just pop into the label writer’s office to ask questions, because they were databasing tags that were decades or centuries old. Sometimes finding the correct answers required researching historical records and venturing into the collection to investigate the specimen packets in person—exciting work for students never before exposed to millions of cataloged specimens in a natural history collection.

Digitization Defined

Digitization is the act of creating a digital record of a specimen that includes scientific names; dates and locations of its collection; the collector’s name; and other relevant data. Each record functions just as a 3×5 card in a catalog, helping researchers locate a single record among millions of similar ones. Digitized specimen records make the search process quick and efficient while enabling researchers to identify patterns and spot anomalies within a collection. With the application of certain formulas, databases can support scientists’ efforts to track species diversity and abundance over time, potentially helping us understand how changing environmental conditions have affected survival and distribution for certain species.

As scientific collections go online in our increasingly digital world, students are taking advantage of the growing digital landscape to broaden their career options. Often funded by grants (the Academy’s botany project is supported by the National Science Foundation), digitization projects may offer openings for students in a number of different fields, including systematics, biology, geology, environmental science, information systems, life sciences, museum studies, and the arts. Already more than comfortable with technology, students can conduct research, compile and input data, learn about best practices in curation, and even take photographs.

They don’t need a ton of background to learn the role. Blase had taken one class on natural history museums (with Academy Assistant Curator of Botany Tatyana Livshultz) in which the students practiced taking digital measurements of plant specimens.

Being affiliated with Drexel University has enabled Academy scientists to meet more students who are interested in natural history and may already have attributes that make them a great fit for digitization work. Through the Drexel cooperative education program, students interview for six-month positions in their fields.

Co-op positions, some of which are paid, enable students to try out real-world job functions and make measurable contributions within their places of employment. Many positions offered at the Academy involve digitization of our scientific collections.

“The six-month co-op gives a set of mental tools and introduces people to what a research museum does,” says Collection Manager of Malacology Paul Callomon. “Students get to ask why we do certain things the way that we do, and that helps staff to constantly reexamine our assumptions.”

Venus Comb Shell
Venus Comb Shell: Murex pecten (Lightfoot, 1786) This shallow-water marine species has built a shell that is as large and hard to bite as possible. The animal creates the spines by forming its flesh into long, narrow tubes and filling them in with shell material. It was first scientifically named in the auction catalog of the collection of the Duchess of Portland in 1786, though it was known in China and Japan as “fish-bone shell” long before that.

Digging Into Data

As scientists digitize specimens with handwritten labels, they often spot gaps in the recorded information. The missing details must be identified for a specimen record to be comparable to others within a database. Often collection managers rely on students to fill in these blanks by parsing data into fields and standardizing geographic data from different countries.

Accuracy is essential, as many digitization projects, including the Academy’s Malacology Digitization Project (funded by the National Science Foundation from 2012–2015), focus solely on type specimens. Designated as the name-bearing specimens when a new species was described, these specimens are used to identify members of their species.

Even before data is entered, scientists must dig into the historical records to confirm that they have the type and investigate whether anyone has reconsidered the specimen’s classification since its naming. Students are trained in this painstaking process, called “forensic reading,” which requires them to apply today’s naming standards to yesterday’s scientific specimen names. Being good at forensic reading requires determination and keen attention to detail.

“We look for students who can recognize patterns and spot anomalies,” Callomon says. “We’re looking for a naturalist with a sharp eye for authenticity.”

Callomon saw this quality in Ellen Wildner during her first interview at the Academy. As a junior studying biology at Drexel University in 2015, Wildner applied and was chosen for a six-month co-op that involved verifying the type status of specimens to be digitized and carrying out the imaging and data entry for each specimen.

Amphidromus quadrasi
Quadras’ Amphidromus: Amphidromus quadrasi (Hidalgo, 1887) The Amphidromus snails of the Philippines and Indonesia are unusual in that—as their name implies—their shells can coil either clockwise or anticlockwise, sometimes even within the same species. They also vary greatly in color and pattern between localities, often making it difficult to define the species. This color form was named versicolor by Fulton in 1896 but is thought to be a local variant of quadrasi. In common with the myriad other animals of the tropical jungles in their region, the habitats of the Amphidromus snails are seriously threatened by agriculture and mining.

Prior to her co-op, Wildner worked in a Drexel lab where she practiced handling and identifying insects. When the opportunity arose to work with specimens at the Academy, Wildner jumped at the chance to explore one of the largest malacology collections in the world. After her co-op, she returned to the Academy as a weekly volunteer and eventually began working in the collection as a full-time employee.

Wildner starts a typical day in the library examining journals that contain descriptions of new species often authored by scientists working in close association with the Academy’s Malacology Department. She notes whether the Academy has the specimens and retrieves them from the collection.

“Once I have the specimens it takes a bit of time to go through the publication and determine whether these were the exact specimens observed at the time of designation,” she says. “I need to verify their status and search for additional publications if necessary.”

After Wildner completes her research, she goes into a camera room to photograph the specimens, returning them to the collection tagged with notes that indicate they’ve been digitized.

“Anything I can do to prevent the destruction and potential loss of type specimens is incredibly important to me,” Wildner says. “By providing images, we are not only making it easier for people around the world to study our specimens, but we are preserving them for future scientific work.”

Taking Pictures

Adding images to the data, a task of increasing priority within the past two decades, enables the public and scientists around the world to search for and view specimens online. Researchers around the world quickly and efficiently consult specimens to determine whether to visit the Academy for additional study. The high-quality images also offer curious amateur naturalists the chance to view the specimens as many times as they like.

“Natural history tends to present itself to the world in books, documents, and scholarly publications,” Callomon says. “We need to be mindful of that and to present collections to people who had no idea about them.”

Teramachi's Slit Shell
Teramachi’s Slit Shell: Bayerotrochus teramachii (Kuroda, 1955) This is a slit shell, one of fewer than 30 surviving species in an ancient family that was abundant in all oceans from the Cambrian to the end of the Cretaceous era. The slit is a natural feature; it forms a duct that channels water out of the animal’s gill cavity. Slit shells have long been known as fossils but were thought extinct before a living one was found for the first time off the West Indies in 1879. They have since been found in South Africa, Australia, Japan, and elsewhere.

Most Academy collections are participating in ongoing digital imaging projects. Academy ichthyologists use high-resolution micro CT (computerized tomography) scans to create 3-D images that can be rotated and sliced into sections digitally, making the images especially useful for examining small specimens. Many departments take high-resolution photographs of specimens using a digital camera and special lighting, while others use flatbed scanners.

The prioritization of imaging has opened doors for photographers and science students looking to make their way into the field of natural history. Xinyi (Amber) Lu was the first co-op to work on the Botany Digitization Project. She photographed lichens and bryophytes, focusing specifically on specimen labels, which were then analyzed by imaging software so that students such as Blase and Coghlan could input and edit the captured data. Along with database development and maintenance, imaging is now part of Lu’s skill set that will help her deliver better work as a research assistant.

Working for a Cause

Without a doubt, parsing specimen data and making sure to avoid typos can be tedious, but students consistently describe their passion for their work. Whether their goals were to explore careers in the sciences or natural history, become better researchers, build their resumes, or learn new skills relevant to future employment, they feel their work is meaningful.

Most college students do not have the opportunity to work within one of the top natural history collections in the world. Not only do Drexel students get to view and handle specimens at the Academy, but they also are helping to safeguard these collections through the creation of digital records. In many cases, scientists will rely on the data students input, the research they conduct, and the photographs they take for years—and even decades—to come.

This article originally appeared in the spring 2016 issue of Academy Frontiers.

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